Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae

Abstract

Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae, we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a "shift" between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a "drift" between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.

Fig. 1.

Neighbor-joining trees showing phylogenetic relationships of 23 V. cholerae strains representing diverse serogroups. (A) All V. cholerae strains based on 1,676 genes (1,370,469 bp). (B) Phylocore genome (PG) clade based on 2,663 genes (2,567,393 bp). (C) Seventh pandemic (7P) clade based on 3,364 genes (3,291,577 bp). Bootstrap supports, as percentage, are indicated at the branching points. Bars represent the numbers of substitution per site, respectively. Only orthologous genes showing >95% nucleotide sequence similarity to those of V. cholerae N16961 were selected. The tree was rooted using Vibrio vulnificus YJ016 and Vibrio parahaemolyticus RIMD 2210633.

Fig. 2.

Schematic representation of various prophages and genetic elements present in the target regions of CTXφ insetion. *, TLC, El Tor type CTXφ, RS1 element are found, but no positional information can be obtained from genome assemblies. †, classical type CTXφ and RS1 are present, but no positional information can be obtained.

Fig. 3.

Genomic representation of genomic islands of both V. cholerae chromosomes. The two circles in the middle represent the genes in V. cholerae O1 El Tor N16961. The inner circle indicates genomic islands found in strain N16961, whereas the outer circles are those absent in strain N16961.

Fig. 4.

Proposed hypothetical evolutionary pathway of the V. cholerae species. Probable insertions and deletions of genomic islands (Table S1) found in 23 V. cholerae strains are indicated by black and red arrows, respectively, along the phylogenetic tree based on genome sequence data. Hypothetical ancestral strains are indicated by open circles.